def do_projection(self, channel, proj_type=None):
proj = ZProjector() ## create projection class
if proj_type is None:
if self.do_z[channel] == "MAX":
proj.setMethod(ZProjector.MAX_METHOD)
elif self.do_z[channel] == "AVG":
proj.setMethod(ZProjector.AVG_METHOD)
else:
print "Dont know how to project this way"
print "Just using a single slice for images!!"
return None
else:
if proj_type == "MAX":
proj.setMethod(ZProjector.MAX_METHOD)
elif proj_type == "AVG":
proj.setMethod(ZProjector.AVG_METHOD)
else:
print "Dont know how to project this way"
print "Just using a single slice for images!!"
return None
proj.setImage(self.stack_imps[channel])
proj.doProjection()
projection = proj.getProjection()
conv = ImageConverter(projection)
conv.convertToGray16()
conv.setDoScaling(False)
self.projections[channel] = projection
self.projections_done[channel] = self.do_z[channel]
def convert(filepath, targetFolder):
imp = IJ.openImage(filepath)
if imp.getType() == ImagePlus.GRAY32:
ic = ImageConverter(imp)
ic.setDoScaling(False)
ic.convertToGray16()
filename = os.path.basename(filepath)
writeZip(imp, os.path.join(targetFolder, filename), title=filename)
else:
syncPrint("Not a 32-bit image: " + filename)
from loci.plugins import BF
from loci.plugins.in import ImporterOptions
import os,sys
path = '/Users/justin/UTS/Research/microscopy/'
filetab = '%s/ijfiles' %path
for l in open(filetab):
f = l.strip().split()
out = f[0]
ch1 = '%s/%s' %(path,f[1])
ch2 = '%s/%s' %(path,f[2])
print('%s: opening %s and %s' %(out,ch1,ch2))
ch1 = ij.IJ.openImage(ch1)
conv = ImageConverter(ch1)
conv.convertToGray16()
# ch1.show()
ch2 = ij.IJ.openImage(ch2)
conv = ImageConverter(ch2)
conv.convertToGray16()
# ch2.show()
# ch1.close()
# ch2.close()
mrg = RGBStackMerge.mergeChannels([ch1, ch2], False)
# mrg.show()
mrgf = '%s/%s.merged.tiff' %(path,out)
ij.IJ.saveAs(mrg,"Tiff",mrgf)
mrg.close()
opts = ImporterOptions()
opts.setId(mrgf)
opts.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE)
